The remediation of soils simultaneously contaminated with organic and inorganic compounds is still a challenging task. The application of metallic nanoparticles, such as zero-valent iron nanoparticles (nZVI), for soil remediation is highly promising, but their effectiveness and potential ecotoxicity must be further investigated. In addition, the performance of nZVI when combined with other remediation strategies is a topic of great interest. Here, we present data on soil chemical (pseudo-total and CaCl2-extractable metal concentrations; petroleum hydrocarbon concentrations) and biological properties (microbial properties and phytotoxicity) after the application of nZVI to soil simultaneously contaminated with Zn, Cu, Cd and diesel, in the absence and presence of other remediation treatments such as the application of an organic amendment and the growth of Brassica napus plants. Soils were artificially contaminated with the abovementioned contaminants. Then, after an aging period of one month, nZVI were applied to the soil and, subsequently, B. napus seeds were sown. Plants were left to grow for one month. Soil samples were collected immediately after artificially contaminating the soil (T1), at sowing (T2) and at harvesting (T3). Overall, the application of nZVI had no effect on contaminant removal, nor on soil microbial parameters. In contrast, it did cause an indirect toxic effect on plant root elongation due to the interaction of nZVI with soil organic matter. These data are useful for researchers and companies interested in the effectiveness and ecotoxicity of zero-valent iron nanoparticles during the remediation of soil contaminated with metals and hydrocarbons, especially when combined with Gentle Remediation Options.